<html>\r
-<head><title>Overview</title></head>\r
+<head><title>Overview Window</title></head>\r
<body>\r
-\r
-<p>Select the overview window to get a navigable image of the whole alignment.\r
+<strong>View→Overview window</strong>\r
+<p>Select the overview window menu item to get a navigable image of the whole alignment.\r
</p>\r
-<p>The window indicates the current viewable region of the alignment, this area \r
- may be adjusted by clicking and dragging with the mouse.</p>\r
+<p>The red box indicates the currently viewed region of the alignment, this \r
+ may be moved by clicking and dragging with the mouse.</p>\r
<p><img src="overview.gif" width="407" height="137"></p>\r
<p> </p>\r
</body>\r
\r
<body>\r
<p><strong>Search</strong></p>\r
-<p>The search box can be displayed by pressing the keys Control and F or selecting\r
- "Search"</p>\r
-Note:\r
+<p>The search box is displayed by pressing Control and F or\r
+ selecting "Find..." from the "Search" menu.</p>\r
+<img src="search.gif">\r
+<p>"Find next" will find the next occurence of the specified\r
+ and adjust the alignment window view to show it, and "Find\r
+ all" highlights all matches for a pattern. The "Create new\r
+ group" is a quick way to highlight and group residues matching\r
+ the specified search pattern throughout the alignment.</p> \r
<ul>\r
- <li>The search will be performed on the selected region. If no region is selected,\r
- the search will operate on the full alignment.</li>\r
- <li>To clear any selection, press the "Escape" key.</li>\r
+<li>The search uses regular expressions. (understands a mixture of\r
+ posix and perl style regex - see below for a summary)</li>\r
+<li>Gaps are ignored when matching the query to the sequences in the\r
+ alignment.</li>\r
+<li>The search is applied to both sequences and their IDs but the "Find next"\r
+ and "Find all" buttons only count the sequence matches.</li>\r
+ <li>If a region is selected, then search will <strong>only</strong>\r
+ be performed on that region. </li>\r
+ <li>To quickly clear the current selection, press the "Escape" key.</li>\r
</ul>\r
-<p>Using the "Create new group" is a quick way to group and highlight\r
- residues with the specified search pattern throughout the alignment.</p>\r
-<p>The search allows regular expression matching. </p>\r
-<p> </p>\r
+<p><strong>A quick Regular Expression Guide</strong></p>\r
+<p>A regular expression is not just a simple text query - although it\r
+can be used like one, the query is not parsed literally, but\r
+interpreted like a series of instructions defining the features of the\r
+match. For example, a simple query like "ACDED" would\r
+match all occurences of that string, but "ACD+ED" matches\r
+both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query\r
+"[ILGVMA]{;5,}" would find stretches of small,\r
+hydrophobic amino acids of at least five residues in length.\r
+</p>\r
+<p> The table\r
+below describes some of the regular expression syntax:<br></p>\r
<table width="100%" border="1">\r
<tr>\r
+ <td width="24%">Regular Expression Element</td>\r
+ <td width="76%">Effect</td>\r
+ </tr>\r
+ <tr>\r
<td width="24%">.</td>\r
- <td width="76%">Any single character.</td>\r
+ <td width="76%">Matches any single character</td>\r
</tr>\r
<tr>\r
<td>[]</td>\r
- <td>Any one of the characters in the brackets</td>\r
+ <td>Matches any one of the characters in the brackets</td>\r
</tr>\r
<tr>\r
<td>^</td>\r
- <td>The start of a line (column 1). </td>\r
+ <td>Matches at the start of an ID or sequence</td>\r
</tr>\r
<tr>\r
<td>$</td>\r
- <td>The end of a line </td>\r
+ <td>Matches at the end of an ID or sequence</td>\r
</tr>\r
<tr>\r
<td>*</td>\r
- <td> Matches zero or more of the preceding characters or expressions. </td>\r
+ <td>Matches if the preceding element matches zero or more times</td>\r
</tr>\r
<tr>\r
<td>?</td>\r
- <td>Matches zero or one of the preceding characters or expressions. </td>\r
+ <td>Matches if the preceding element matched once or not at all</td>\r
</tr>\r
<tr>\r
<td>+</td>\r
- <td>Matches one or more of the preceding characters or expressions. </td>\r
+ <td>Matches if the preceding element matched at least once</td>\r
</tr>\r
<tr>\r
<td>{count}</td>\r
- <td> Matches the specified number of the preceding characters or expressions.\r
+ <td>Matches if the preceding element matches a specified number of\r
+ times\r
</td>\r
</tr>\r
<tr>\r
<td>{min,}</td>\r
- <td> Matches at least the specified number of the preceding characters or\r
- expressions.</td>\r
+ <td> Matches at least the specified number of the preceding element.</td>\r
</tr>\r
<tr>\r
<td>{min,max} </td>\r
- <td>Matches between min and max of the preceding characters or expressions.</td>\r
+ <td>Matches if the preceding element matches between min and max\r
+ number of times.</td>\r
</tr>\r
</table>\r
</body>\r
<html>\r
<head><title>Sequence Features</title></head>\r
<body>\r
-<p><strong>Sequence Features</strong></p>\r
-<p>This displays Uniprot sequence features on the alignment if a 100% sequence\r
- match is found. </p>\r
-<p>The first step in this process is to match the id (name) of each sequence with\r
- Uniprot. If there is no match, a Blast search is performed to try to obtain\r
- the Uniprot Id for each sequence. You will be notified of any 100% matches with\r
- Uniprot, which you must manually assign to each sequence in your input alignment,\r
- then save the file.</p>\r
+<p><strong>View→Sequence Features</strong></p>\r
+<p>When this option is selected, sequence features extracted from the\r
+ <a href="http://www.ebi.uniprot.org/">Uniprot</a> record for each\r
+ sequence are displayed on the alignment.</p>\r
+<p>Currently, sequence features are rendered in red or blue, dependent\r
+ upon their type:</p><ul>\r
+ <li>Features associated with a particular residue are coloured\r
+ red<br><italic>e.g. an active site residue</italic></li>\r
+ <li>Features which span a region are coloured blue<br>\r
+<italic>e.g. a region of sequence with known structure</italic></p>\r
+<p>More information about the feature is given in a tooltip, which are\r
+ viewed by moving the mouse pointer over a sequence feature. The\r
+ associated text for the feature will then be displayed in a small\r
+ label will appear near the pointer.</p>\r
+<p>After the Sequence Features option is selected, there may be some delay before\r
+ the features are actually rendered, as jalview must first determine if a\r
+ sequence is contained in uniprot and then retrieve its sequence\r
+ record. This delay should only happen once for a particular\r
+ alignment, as jalview caches uniprot records in a file in your home\r
+ directory called '.jalview.uniprot.xml'.\r
+\r
+<p>The first step in this process is to try to use the ID (name) of\r
+ each sequence as an ID search in Uniprot. If there is no match, The\r
+ EBI Blast search is used in an attempt to obtain the Uniprot Id for\r
+ each sequence. You will be notified of any 100% matches with\r
+ Uniprot, but you must then manually change the name of the sequence,\r
+ by right clicking on the sequence ID and selecting\r
+ Sequence→Edit Name, before Jalview will show its sequence\r
+ features.<ul>\r
+ <li>remember to save your alignment if you have updated any of the\r
+ sequence IDs!\r
+ </li>\r
+ </ul></p>\r
<p>\r
- The input sequence will be matched with the returned Uniprot record, the start\r
- and end residues can then be correctly assigned to each sequence. </p>\r
-<p>Sequence features which are 1 residue in length are coloured red. Features\r
- which span a region are coloured blue. </p>\r
-<p>By moving the mouse pointer over a sequence feature on the alignment a small\r
- label will appear with the description of that sequence feature.</p>\r
-<p>A local cache of retrieved uniprot entries is recorded on your local machine.\r
-</p>\r
+ If a uniprot record (or set of records) is found for a sequence,\r
+ then the sequence in aligned to the one in the Uniprot record\r
+ to determine the correct start and end residue positions that will be\r
+ displayed when the 'Show Full Sequence ID' option is set.</p>\r
</body>\r
</html>\r
<head><title>Wrap Alignment</title></head>\r
\r
<body>\r
-<p><strong>Wrap alignment </strong></p>\r
+<p><strong>View→Wrap alignment </strong></p>\r
<p>Use this feature to wrap an alignment to the screen width. </p>\r
<p>All output (HTML, Printing, JPG etc) will also be in this wrapped format.</p>\r
<p>This is most useful when looking at alignments with less than 20 sequences.\r
-<html>\r
-<head><title>What's new</title></head>\r
-<body>\r
-<p><strong>What's new</strong> </p>\r
-<p>If you can read this then you'll already have seen some of the recent changes\r
- made to Jalview.<br>\r
- Jalview takes advantage of some of the more recent user interface developments\r
- in the Java programming language. For instance Jalview is now a multi windowed\r
- application, this keeps all your Jalview windows neatly together in one main\r
- application window. </p>\r
-<p>If you were familiar with the original Jalview, here is a list of important\r
- features you should know about the current development:</p>\r
-<ul>\r
- <li>Editing sequences is no longer the default when mouse clicking the alignment.\r
- Instead, mouse clicking on the alignment will create a "selection region"\r
- which may be full sequences or groups of residues.</li>\r
- <li>To edit a sequence, the "Shift" key must be held down</li>\r
- <li>To edit groups, either the "Alt" key or the "Control"\r
- key must be held down.</li>\r
- <li>Colours maybe applied to the background, ie the whole alignment, or to selected\r
- regions. If the tickbox "Apply colour to all groups" is ticked (this\r
- is the default), then the colour will be applied to all groups.</li>\r
- <li>Use the right mouse button (apple and click on the mac) to define a selected\r
- region on the alignment as a new group. </li>\r
- <li>Conservation is automatically updated whenever the alignment is edited</li>\r
- <li>There is no "quick draw" option</li>\r
- <li>Edits can be undone! (and redone)</li>\r
-</ul>\r
-</body>\r
-</html>\r
+<html>
+<head><title>What's new ?</title></head>
+<body>
+<p><strong>What's new ?</strong> </p>
+<p>If you are reading this then you will already have seen some of the recent changes
+ made to Jalview.<br>
+ Jalview takes advantage of some of the more recent user interface developments
+ in the Java programming language. For instance Jalview is now a multi windowed
+ application, this keeps all your Jalview windows neatly together in one main
+ application window. </p>
+<p>If you were familiar with the original Jalview, here is a list of important
+ features you should know about the current development:</p>
+<ul>
+ <li>Editing sequences is no longer the default when mouse clicking the alignment.
+ Instead, mouse clicking on the alignment creates a "selection region"
+ which may be full sequences or groups of residues.</li>
+ <li>To insert or edit the gaps in one sequence in alignment, the
+ "Shift" key must be held down when dragging the mouse.</li>
+ <li>To insert or edit gaps for a group of sequences, the
+ "Alt" key (or in X windows the "Control"
+ key) must be held down.</li>
+ <li>Selecting colour schemes in the colour menu either sets just the
+ "background" colourscheme for the alignment, or - when
+ the tickbox "Apply colour to all groups" is ticked,
+ applies the scheme to the background and all groups defined on the alignment.</li>
+ <li>Use the right mouse button (apple and click on the Mac) whilst
+ the pointer is within the selection area to access the "define" region menu to
+ define a new region, give it a name, and change its colourscheme and display
+ properties.</li>
+ <li>Conservation is automatically updated whenever the alignment is edited</li>
+ <li>There is no "quick draw" option</li>
+ <li>Edits can be undone, and redone!</li>
+</ul>
+</body>
+</html>
git://source.jalview.org / jalview.git / commitdiff
